The government pushed through its plans for secret court hearings on Monday night, defeating amendments tabled by the Labour frontbench with significant majorities.

In the first division on a proposal aimed at introducing further conditions before closed material procedures (CMPs) could be used in civil courts, Labour and coalition rebels lost by 225 to 298 votes – a government majority of 73.

A second Labour proposal, requiring judges to balance the interests of national security against "public interest in the fair and open administration of justice", was lost by 226 to 297 – a government majority of 71.

Over the course of the bill the government has already made a number of concessions in an attempt to win over Liberal Democrats and other opponents. But on Monday night civil liberties campaigners vowed to continue fighting government plans for secret court hearings in sensitive national security cases after MPs rejected stronger safeguards.

"The opposition to turning British courts into secret commissions continues. Once again, we look to the House of Lords to defeat secret courts and defend the rule of law."

Clare Algar, executive director of Reprieve, said: "This has been a dark night for British justice.

"These plans for secret courts were always dangerous and unnecessary, but the failure of even minor attempts to modify the bill means that it is even worse than when it first reached the House of Commons.

"MPs must now vote against the bill altogether if they want to defend British justice.

"Should that fail, the House of Lords will be the only thing standing in the way of plans which would mean the end of the right to a fair trial in a vast range of civil cases."

After the vote, the Lib Dem MP Sir Menzies Campbell, who is member of the intelligence and security committee, said he had supported the government because "this is necessary legislation".

He told BBC radio: "What this bill does is ensure that the government can't close off any particular line of investigation."

But Sadiq Khan, the shadow justice secretary, told the Commons that while he accepted the difficulty of "reconciling the issues of justice and security" the legislation was not "proportionate to the scale of the problem".

During the debate, government plans for secret courts received strong endorsement from a former Labour home secretary, while Tory rebels warned that the proposals "deny open justice".

In the closing Commons debate at the report stage of the justice and security bill, MPs wrangled for more than four hours over the complex detail of how judges can fairly conduct trials involving national security which withhold evidence from one side in a case.

Khan introduced a series of amendments aimed at putting in place "appropriate checks and balances" on the expansion of secret hearings, known as closed material procedures (CMPs), into the civil courts.

Khan said the government had "unpicked" changes made to the bill in the Lords and Labour's amendments sought to restore the improvements made by peers.

He said: "Our amendments seek to put in place appropriate checks and balances on the use of CMPs.

"We do not underestimate the difficulties of reconciling the issues of justice and security as contained in the title of the bill, but it's difficult, not impossible.

"By putting in place appropriate measures, we believe the use of CMPs will be proportionate to the scale of the problem they are seeking to address."

But his party colleague Jack Straw, who served both as home and foreign secretary in Labour administrations, claimed amendments put forward by his own front bench ran the risk of deterring agents working for the secret and intelligence services from passing on vital information. Such agents, he said, would be in danger of being identified under Labour's amendments.

"Let's remind ourselves – and this isn't scaremongering, it happens to be true [that without such intelligence] – there would have been scores of really serious atrocities killing your constituents and many others," he said.

"And when we came to explain why we landed up in that situation and said 'well we thought there was no possibility other than to have information in open court in all circumstances', they'll say 'well thanks very much: my relative, my wife, my child has just died'.

"That's the dilemma here, and it's not an abstract one, it's an absolutely real one."

Conversely, some of the most powerful speeches against the government's bill came from the Conservative benches.

Andrew Tyrie, the respected Tory chair of the Treasury select committee, said it was "rare" that he agreed with the opposition and disagreed with his own front bench, but the amendments tabled by the bill's opponents were not "technical".

He added: "They are really about the society we live in: whether people can hear the evidence against them, whether we can keep the safeguards we have had for generations … and above all they are about what values we as a country are seeking to espouse and export."

Earlier Richard Shepherd, a strongly libertarian Tory MP, opposed the government's proposal to limit debate for the second reading to two days this week – though the motion was passed without needing a vote.

"This bill seeks to do something very profound indeed," he said. "It seeks to deny open justice on the basis that we'll get better justice by making it covert or secret."

He was supported by another Tory, Peter Bone, a more frequent rebel, who called the issue a "constitutional matter" which was "extremely important".

Ken Clarke, the minister without portfolio who is steering the legislation through parliament, claimed he had made unprecedented amendments to reassure critics, including giving judges "unfettered" power to decide whether cases should be heard in private or not, and giving them power to return to open court if special advocates for the defence successfully challenged the need for evidence to be heard in private.

He accused critics of inventing new conditions and amendments to try to stop the use of closed material procedures altogether.

"Critics somehow take the view it's a lesser evil to keep paying out millions of pounds [rather than use] closed material procedures," he said.

Earlier Clarke told the BBC Radio 4 World at One programme: "This is less than perfect. Of course if this was a road traffic accident I'd be absolutely outraged: the question is when we're threatened by jihadists in this country can we possibly give public details of the operations we're carrying out, our co-operation with other agencies in America and elsewhere – of course we can't."

Sir Malcom Rifkind, the Tory chairman of the intelligence and security committee, said he was bemused by civil liberties groups' sudden affection for public interest immunity certificates – a court procedure that excludes sensitive evidence altogether from court cases.

PII certificates, he said, had previously been greeted by "howls of execration". Closed material procedures would also benefit plaintiffs in a case, Rifkind added.